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Improving the Positive Predictive Value of Non-Invasive Prenatal Screening (NIPS)

View Article: PubMed Central - PubMed

ABSTRACT

We evaluated performance characteristics of a laboratory-developed, non-invasive prenatal screening (NIPS) assay for fetal aneuploidies. This assay employs massively parallel shotgun sequencing with full automation. GC sequencing bias correction and statistical smoothing were performed to enhance discrimination of affected and unaffected pregnancies. Maternal plasma samples from pregnancies with known aneuploidy status were used for assay development, verification, and validation. Assay verification studies using 2,085 known samples (1873 unaffected, 69 trisomy 21, 20 trisomy 18, 17 trisomy 13) demonstrated complete discrimination between autosomal trisomy (Z scores >8) and unaffected (Z scores <4) singleton pregnancies. A validation study using 552 known samples (21 trisomy 21, 10 trisomy 18, 1 trisomy 13) confirmed complete discrimination. Twin pregnancies showed similar results. Follow-up of abnormal results from the first 10,000 clinical samples demonstrated PPVs of 98% (41/42) for trisomy 21, 92% (23/25) for trisomy 18, and 69% (9/13) for trisomy 13. Adjustment for causes of false-positive results identified during clinical testing (eg, maternal duplications) improved PPVs to 100% for trisomy 21 and 96% for trisomy 18. This NIPS test demonstrates excellent discrimination between trisomic and unaffected pregnancies. The PPVs obtained in initial clinical testing are substantially higher than previously reported NIPS methods.

No MeSH data available.


Related in: MedlinePlus

Z scores of the laboratory-developed noninvasive prenatal assay for                            trisomies 21, 18, and 13 before (raw) and after correction for GC                            content and statistical smoothing using a proprietary software                            algorithm.                        The assay provided complete discrimination between affected and                            unaffected pregnancies for trisomy 21, even without adjustments. GC                            correction and statistical smoothing eliminated the substantial overlap                            between affected and unaffected pregnancies for trisomies 18 and 13, and                            enhanced separation for trisomy 21.
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pone.0167130.g002: Z scores of the laboratory-developed noninvasive prenatal assay for trisomies 21, 18, and 13 before (raw) and after correction for GC content and statistical smoothing using a proprietary software algorithm. The assay provided complete discrimination between affected and unaffected pregnancies for trisomy 21, even without adjustments. GC correction and statistical smoothing eliminated the substantial overlap between affected and unaffected pregnancies for trisomies 18 and 13, and enhanced separation for trisomy 21.

Mentions: Maternal Microduplications: Early during clinical testing we encountered 2 cases with intermediate Z scores between 3 and 8 (Fig 2). One had a Z score of 5.11 for trisomy 21 and another had a Z score of 6.93 for trisomy 18 (Fig 2). We had recently read a report describing “false-positive” NIPS results due to maternal microduplications [21] and decided to use chromosomal ideograms to investigate whether these intermediate Z scores represented maternal microduplications. Fig 3 shows the ideogram for a typical NIPS result from a fetus confirmed to have trisomy 21. In both of our cases, the ideograms clearly showed that the duplications were in a small portion of the affected chromosomes (Fig 4). With permission from the ordering physicians, we performed microarray analysis on the maternal buffy coat cells, which confirmed the maternal microduplication on chromosome 21 (Fig 5) and 18 (Figs 6 and 7). Henceforth, we examined the ideogram for each chromosome with an elevated Z score before reporting an abnormal result, to ensure the entire chromosome is duplicated and the result is not due to a maternal microduplication. The cumulative data regarding our experiences with maternal microduplications has been submitted elsewhere.


Improving the Positive Predictive Value of Non-Invasive Prenatal Screening (NIPS)
Z scores of the laboratory-developed noninvasive prenatal assay for                            trisomies 21, 18, and 13 before (raw) and after correction for GC                            content and statistical smoothing using a proprietary software                            algorithm.                        The assay provided complete discrimination between affected and                            unaffected pregnancies for trisomy 21, even without adjustments. GC                            correction and statistical smoothing eliminated the substantial overlap                            between affected and unaffected pregnancies for trisomies 18 and 13, and                            enhanced separation for trisomy 21.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5382935&req=5

pone.0167130.g002: Z scores of the laboratory-developed noninvasive prenatal assay for trisomies 21, 18, and 13 before (raw) and after correction for GC content and statistical smoothing using a proprietary software algorithm. The assay provided complete discrimination between affected and unaffected pregnancies for trisomy 21, even without adjustments. GC correction and statistical smoothing eliminated the substantial overlap between affected and unaffected pregnancies for trisomies 18 and 13, and enhanced separation for trisomy 21.
Mentions: Maternal Microduplications: Early during clinical testing we encountered 2 cases with intermediate Z scores between 3 and 8 (Fig 2). One had a Z score of 5.11 for trisomy 21 and another had a Z score of 6.93 for trisomy 18 (Fig 2). We had recently read a report describing “false-positive” NIPS results due to maternal microduplications [21] and decided to use chromosomal ideograms to investigate whether these intermediate Z scores represented maternal microduplications. Fig 3 shows the ideogram for a typical NIPS result from a fetus confirmed to have trisomy 21. In both of our cases, the ideograms clearly showed that the duplications were in a small portion of the affected chromosomes (Fig 4). With permission from the ordering physicians, we performed microarray analysis on the maternal buffy coat cells, which confirmed the maternal microduplication on chromosome 21 (Fig 5) and 18 (Figs 6 and 7). Henceforth, we examined the ideogram for each chromosome with an elevated Z score before reporting an abnormal result, to ensure the entire chromosome is duplicated and the result is not due to a maternal microduplication. The cumulative data regarding our experiences with maternal microduplications has been submitted elsewhere.

View Article: PubMed Central - PubMed

ABSTRACT

We evaluated performance characteristics of a laboratory-developed, non-invasive prenatal screening (NIPS) assay for fetal aneuploidies. This assay employs massively parallel shotgun sequencing with full automation. GC sequencing bias correction and statistical smoothing were performed to enhance discrimination of affected and unaffected pregnancies. Maternal plasma samples from pregnancies with known aneuploidy status were used for assay development, verification, and validation. Assay verification studies using 2,085 known samples (1873 unaffected, 69 trisomy 21, 20 trisomy 18, 17 trisomy 13) demonstrated complete discrimination between autosomal trisomy (Z scores >8) and unaffected (Z scores <4) singleton pregnancies. A validation study using 552 known samples (21 trisomy 21, 10 trisomy 18, 1 trisomy 13) confirmed complete discrimination. Twin pregnancies showed similar results. Follow-up of abnormal results from the first 10,000 clinical samples demonstrated PPVs of 98% (41/42) for trisomy 21, 92% (23/25) for trisomy 18, and 69% (9/13) for trisomy 13. Adjustment for causes of false-positive results identified during clinical testing (eg, maternal duplications) improved PPVs to 100% for trisomy 21 and 96% for trisomy 18. This NIPS test demonstrates excellent discrimination between trisomic and unaffected pregnancies. The PPVs obtained in initial clinical testing are substantially higher than previously reported NIPS methods.

No MeSH data available.


Related in: MedlinePlus